From d4411755a3ca05f138a75e330ef3cff2023a9c66 Mon Sep 17 00:00:00 2001
From: RobJY <robert.jay.young@gmail.com>
Date: Tue, 7 May 2024 16:48:11 -0400
Subject: [PATCH] added nf-validation to check for most file existence

---
 assets/schema_input_cycle.json                           | 8 +++++++-
 assets/schema_input_sample.json                          | 4 ++++
 subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf | 4 ++--
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/assets/schema_input_cycle.json b/assets/schema_input_cycle.json
index 9eb8e1f..c479c34 100644
--- a/assets/schema_input_cycle.json
+++ b/assets/schema_input_cycle.json
@@ -22,17 +22,23 @@
             },
             "image_tiles": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
-                "errorMessage": "Need to provide a path to a directory containing image files"
+                "exists": true,
+                "errorMessage": "Need to provide a path to image file(s)"
             },
             "dfp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
             },
             "ffp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
             }
         },
diff --git a/assets/schema_input_sample.json b/assets/schema_input_sample.json
index 113ef55..7122afa 100644
--- a/assets/schema_input_sample.json
+++ b/assets/schema_input_sample.json
@@ -24,12 +24,16 @@
             },
             "dfp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
             },
             "ffp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
             }
         },
diff --git a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
index 2fb5700..21cd0e1 100644
--- a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
@@ -264,7 +264,7 @@ def validateInputSamplesheetRow ( row, mode ) {
         if (row.size() >= 3 && row[2] != []) {
             def file_list = row[2].split(" ")
             file_list.each { curr_file ->
-                def curr_path = new File(row[1].toString() + "/" + curr_file)
+                def curr_path = file(row[1].toString() + "/" + curr_file)
                 if (!curr_path.exists()) {
                     error("Error: file in samplesheet not found: $curr_path")
                 }
@@ -317,7 +317,7 @@ def make_ashlar_input_sample( samplesheet_row ) {
         }
         cycle_images = samplesheet_row[index_sample_cycle_images].split(' ').collect{ "${tmp_path}${it}" }
         cycle_images.each{ file_path ->
-            def file_test = new File(file_path)
+            def file_test = file(file_path)
             if (!file_test.exists()) {
                 Nextflow.error("Error: ${file_path} does not exist!")
             }